Metadata-Version: 1.2
Name: sequana-demultiplex
Version: 0.9.1
Summary: Pipeline that runs bcl2fastq and creates additional plots within a Snakemake workflow
Home-page: https://github.com/sequana/
Author: cokelaer
Author-email: thomas.cokelaer@pasteur.fr
Maintainer: cokelaer
Maintainer-email: thomas.cokelaer@pasteur.fr
License: new BSD
Description: This is is the **demultiplex** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ projet
        
        :Overview: Runs bcl2fastq on raw BCL data and create some QC plots to ease the QC step
        :Input: A valid Illumina base calling directory
        :Output: a set of PNG files and the expected FastQ files
        :Status: production
        :Citation: Cokelaer et al, (2017), 'Sequana': a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI https://doi:10.21105/joss.00352
        
        
        Installation
        ~~~~~~~~~~~~
        
        You must install Sequana first::
        
            pip install sequana
        
        Then, just install this package::
        
            pip install sequana_demultiplex
        
        Usage
        ~~~~~
        
        ::
        
            sequana_pipelines_demultiplex --help
            sequana_pipelines_demultiplex --working-directory DATAPATH --bcl-directory bcldata
        
        This creates a directory **fastq**. You just need to execute the pipeline::
        
            cd demutliplex
            sh demutliplex.sh  # for a local run
        
        This launch a snakemake pipeline. If you are familiar with snakemake, you can retrieve the demutliplex.rules and config.yaml files and then execute the pipeline yourself with specific parameters::
        
            snakemake -s demutliplex.rules --cores 4 --stats stats.txt
        
        Or use `sequanix <https://sequana.readthedocs.io/en/master/sequanix.html>`_ interface.
        
        Requirements
        ~~~~~~~~~~~~
        
        This pipelines requires the following executable(s):
        
        - bcl2fastq 2.20.0
        
        
        .. image:: https://raw.githubusercontent.com/sequana/sequana_demultiplex/master/sequana_pipelines/demultiplex/dag.png
        
        
        Details
        ~~~~~~~~~
        
        This pipeline runs bcl2fastq 2.20 and creates a set of diagnostics plots to help
        deciphering common issues such as missing index and sample sheet errors. 
        
        
        
        Rules and configuration details
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        Here is the `latest documented configuration file <https://raw.githubusercontent.com/sequana/sequana_demutliplex/master/sequana_pipelines/demutliplex/config.yaml>`_
        to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file. 
        
        Changelog
        ~~~~~~~~~
        
        * 0.9.1 Make the merging options compulsory. Users must tell whether they want to
          merge the lanes or not. This avoid to do the merging or not whereas the
          inverse was expected.
        * 0.8.6 Uses 64G/biomics queue and 16 cores on a SLURM scheduler
        
        
Keywords: bcl2fastq, Illumina, bcl, fastq, demultiplexing, base caller,snakemake,sequana
Platform: Linux
Platform: Unix
Platform: MacOsX
Platform: Windows
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: End Users/Desktop
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Scientific/Engineering :: Physics
